YCFH_ECOLI
ID YCFH_ECOLI Reviewed; 265 AA.
AC P0AFQ7; P37346; P78057;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Uncharacterized metal-dependent hydrolase YcfH {ECO:0000305};
DE EC=3.1.-.- {ECO:0000305};
GN Name=ycfH; OrderedLocusNames=b1100, JW1086;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-104.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=8509334; DOI=10.1128/jb.175.12.3812-3822.1993;
RA Carter J.R., Franden M.A., Aebersold R.H., McHenry C.S.;
RT "Identification, isolation, and characterization of the structural gene
RT encoding the delta' subunit of Escherichia coli DNA polymerase III
RT holoenzyme.";
RL J. Bacteriol. 175:3812-3822(1993).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-43.
RC STRAIN=K12;
RX PubMed=8505303; DOI=10.1016/s0021-9258(19)50264-2;
RA Dong Z., Onrust R., Skangalis M., O'Donnell M.;
RT "DNA polymerase III accessory proteins. I. holA and holB encoding delta and
RT delta'.";
RL J. Biol. Chem. 268:11758-11765(1993).
RN [6]
RP FUNCTION AS A DEACETYLASE, AND COFACTOR.
RX PubMed=19332551; DOI=10.1074/jbc.m808173200;
RA Wydau S., van der Rest G., Aubard C., Plateau P., Blanquet S.;
RT "Widespread distribution of cell defense against D-aminoacyl-tRNAs.";
RL J. Biol. Chem. 284:14096-14104(2009).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH ZINC IONS.
RG New York structural genomix research consortium (NYSGXRC);
RT "Crystal structure of ycfH, tatD homolog from Escherichia coli.";
RL Submitted (FEB-2009) to the PDB data bank.
CC -!- FUNCTION: Has D-tyrosyl-tRNA deacylase activity in vitro.
CC {ECO:0000269|PubMed:19332551}.
CC -!- COFACTOR:
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:19332551};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:19332551};
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:19332551};
CC Note=Binds 2 divalent metal cations per subunit. {ECO:0000269|Ref.7};
CC -!- INTERACTION:
CC P0AFQ7; P15877: gcd; NbExp=2; IntAct=EBI-560527, EBI-545666;
CC -!- SIMILARITY: Belongs to the metallo-dependent hydrolases superfamily.
CC TatD-type hydrolase family. {ECO:0000305}.
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DR EMBL; U00096; AAC74184.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35907.1; -; Genomic_DNA.
DR EMBL; L01483; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; L04577; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; A64854; A64854.
DR RefSeq; NP_415618.1; NC_000913.3.
DR RefSeq; WP_000480245.1; NZ_STEB01000016.1.
DR PDB; 1YIX; X-ray; 1.90 A; A/B=1-265.
DR PDBsum; 1YIX; -.
DR AlphaFoldDB; P0AFQ7; -.
DR SMR; P0AFQ7; -.
DR BioGRID; 4260943; 192.
DR DIP; DIP-48157N; -.
DR IntAct; P0AFQ7; 9.
DR STRING; 511145.b1100; -.
DR jPOST; P0AFQ7; -.
DR PaxDb; P0AFQ7; -.
DR PRIDE; P0AFQ7; -.
DR EnsemblBacteria; AAC74184; AAC74184; b1100.
DR EnsemblBacteria; BAA35907; BAA35907; BAA35907.
DR GeneID; 66670634; -.
DR GeneID; 945656; -.
DR KEGG; ecj:JW1086; -.
DR KEGG; eco:b1100; -.
DR PATRIC; fig|1411691.4.peg.1168; -.
DR EchoBASE; EB2209; -.
DR eggNOG; COG0084; Bacteria.
DR HOGENOM; CLU_031506_4_0_6; -.
DR InParanoid; P0AFQ7; -.
DR OMA; DGPYEYR; -.
DR PhylomeDB; P0AFQ7; -.
DR BioCyc; EcoCyc:EG12303-MON; -.
DR EvolutionaryTrace; P0AFQ7; -.
DR PRO; PR:P0AFQ7; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0004536; F:deoxyribonuclease activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR CDD; cd01310; TatD_DNAse; 1.
DR InterPro; IPR018228; DNase_TatD-rel_CS.
DR InterPro; IPR015991; Hydrolase_TatD-type.
DR InterPro; IPR032466; Metal_Hydrolase.
DR InterPro; IPR001130; TatD-like.
DR Pfam; PF01026; TatD_DNase; 1.
DR PIRSF; PIRSF005902; DNase_TatD; 1.
DR SUPFAM; SSF51556; SSF51556; 1.
DR TIGRFAMs; TIGR00010; TIGR00010; 1.
DR PROSITE; PS01137; TATD_1; 1.
DR PROSITE; PS01091; TATD_3; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Metal-binding; Reference proteome.
FT CHAIN 1..265
FT /note="Uncharacterized metal-dependent hydrolase YcfH"
FT /id="PRO_0000201995"
FT BINDING 7
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000269|Ref.7"
FT BINDING 9
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000269|Ref.7"
FT BINDING 94
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000269|Ref.7"
FT BINDING 94
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000269|Ref.7"
FT BINDING 130
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000269|Ref.7"
FT BINDING 155
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000269|Ref.7"
FT BINDING 205
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000269|Ref.7"
FT CONFLICT 97
FT /note="L -> Q (in Ref. 4)"
FT /evidence="ECO:0000305"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:1YIX"
FT HELIX 10..12
FT /evidence="ECO:0007829|PDB:1YIX"
FT TURN 15..18
FT /evidence="ECO:0007829|PDB:1YIX"
FT HELIX 22..31
FT /evidence="ECO:0007829|PDB:1YIX"
FT STRAND 34..39
FT /evidence="ECO:0007829|PDB:1YIX"
FT HELIX 44..54
FT /evidence="ECO:0007829|PDB:1YIX"
FT STRAND 60..64
FT /evidence="ECO:0007829|PDB:1YIX"
FT HELIX 77..84
FT /evidence="ECO:0007829|PDB:1YIX"
FT STRAND 89..98
FT /evidence="ECO:0007829|PDB:1YIX"
FT HELIX 106..123
FT /evidence="ECO:0007829|PDB:1YIX"
FT STRAND 127..133
FT /evidence="ECO:0007829|PDB:1YIX"
FT HELIX 135..144
FT /evidence="ECO:0007829|PDB:1YIX"
FT HELIX 147..149
FT /evidence="ECO:0007829|PDB:1YIX"
FT STRAND 152..154
FT /evidence="ECO:0007829|PDB:1YIX"
FT HELIX 161..168
FT /evidence="ECO:0007829|PDB:1YIX"
FT TURN 169..171
FT /evidence="ECO:0007829|PDB:1YIX"
FT STRAND 173..176
FT /evidence="ECO:0007829|PDB:1YIX"
FT HELIX 178..181
FT /evidence="ECO:0007829|PDB:1YIX"
FT HELIX 186..194
FT /evidence="ECO:0007829|PDB:1YIX"
FT HELIX 197..199
FT /evidence="ECO:0007829|PDB:1YIX"
FT STRAND 200..202
FT /evidence="ECO:0007829|PDB:1YIX"
FT HELIX 221..223
FT /evidence="ECO:0007829|PDB:1YIX"
FT HELIX 224..235
FT /evidence="ECO:0007829|PDB:1YIX"
FT HELIX 239..253
FT /evidence="ECO:0007829|PDB:1YIX"
FT HELIX 258..261
FT /evidence="ECO:0007829|PDB:1YIX"
SQ SEQUENCE 265 AA; 29809 MW; 722C9450157620C5 CRC64;
MFLVDSHCHL DGLDYESLHK DVDDVLAKAA ARDVKFCLAV ATTLPGYLHM RDLVGERDNV
VFSCGVHPLN QNDPYDVEDL RRLAAEEGVV ALGETGLDYY YTPETKVRQQ ESFIHHIQIG
RELNKPVIVH TRDARADTLA ILREEKVTDC GGVLHCFTED RETAGKLLDL GFYISFSGIV
TFRNAEQLRD AARYVPLDRL LVETDSPYLA PVPHRGKENQ PAMVRDVAEY MAVLKGVAVE
ELAQVTTDNF ARLFHIDASR LQSIR
